The exit status of the task that caused the workflow execution to fail was: 255.
The full error message was:
Error executing process > 'callVariants (8)' Caused by: Process `callVariants (8)` terminated with an error exit status (255) Command executed: echo "Starting BCFTools from within the container for STAT1_STAT1_HUMAN.H11MO.0.A on dataset JD32HPP..." bcftools mpileup -Ou -f "input-dir-cluster/refs/GRCh38_no_alt_GCA_000001405.15.fasta.gz" -T "STAT1_STAT1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed" -b "JD32HPP.bamlist.txt" --annotate FORMAT/AD,FORMAT/DP | bcftools call -Ou -mv | bcftools filter -i'QUAL>10' | bcftools +fill-tags - -- -t AF,VAF > "STAT1_STAT1_HUMAN.H11MO.0.A_qualgt10.var.flt.VAF.allTFBS_JD32HPP.vcf" Command exit status: 255 Command output: Starting BCFTools from within the container for STAT1_STAT1_HUMAN.H11MO.0.A on dataset JD32HPP... Command error: [E::fai_build3_core] Failed to open the file input-dir-cluster/refs/GRCh38_no_alt_GCA_000001405.15.fasta.gz : No such file or directory Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid Failed to read from standard input: unknown file type Failed to read from standard input: unknown file type Failed to read from standard input: unknown file type Work dir: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a1/f7d6a1945c591e28cd713d1afb137c Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
nextflow run -resume main.nf --run_mode subset --dataset_id_list input-dir-cluster/manifests/dataset-manifest-heme-cancers.txt --genome_fasta input-dir-cluster/refs/GRCh38_no_alt_GCA_000001405.15.fasta.gz --output_dir output-dir-cluster -c nextflow_cluster.config -with-dag workflow-reports/dag-20240228-11.11.html -with-report workflow-reports/report-20240228-11.11.html -with-timeline workflow-reports/timeline-20240228-11.11.html4af21cf2ab88a8442835b8986f4f9a49140920df-0168-40f6-86d5-6f6c04264f45These plots give an overview of the distribution of resource usage for each process.
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